Polypeptides for identifying in vitro and preventing staphyloccocal infections on joint prostheses and other implanted foreign materials

ABSTRACT

The invention concerns novel polypeptides, or parts or variants of the novel polypeptides, the use of sequences encoding the polypeptides and the use of antibodies directed against the polypeptides in the field of in vitro diagnosis of a  Staphylococcus epidermidis  and/or  Staphylococcus aureus  infection on foreign material implanted in the body.

The present invention relates to a tool for serological multiparameter diagnosis of staphylococcal infections on joint prostheses (for example infection on a hip, elbow, knee, ankle prosthesis, etc.) and, more generally, diagnosis of staphylococcal infections on foreign material implanted in the body.

In particular, the invention comprises the identification of novel polynucleotides and polypeptides as well as the production, optimisation and use thereof, on the one hand within the field of diagnosing infections on foreign material (joint prostheses for example) involving Staphylococcus aureus and/or Staphylococcus epidermidis and, on the other hand, within the field of producing vaccines against said different agents.

Infections on joint prostheses are a major problem in public health. Hundreds of thousands of joint prostheses are implanted worldwide every year and millions of people have one or more (Lew et Waldvogel, 1997, Osteomyelitis, N Engl J Med 336:999-1007). In the United States of America, it is estimated that approximately 430,000 total hip prostheses (THPs) and total knee prostheses (TKPs) are implanted every year (Berbari et al., 1998, Clin Infect. Dis., 27:1247-1254). In Norway and Sweden, the only countries in which there is a register of prostheses, 250,000 THPs were implanted within the space of ten years between 1987 and 1996 (Lidgren, 2001, Joint prosthetic infections: a success story, Acta Othop Scand 72:553-556). In France, according to the French Society of Orthopaedics, the number of prostheses implanted every year is approximately 100,000 for THPs and 25,000 for TKPs (National Agency for Accreditation and Evaluation in Health, 2000). These figures will continue to rise in future owing to ageing populations (implantation of THPs) and obesity-related problems (implantation of TKPs) in developed countries.

Despite the considerable progress made in recent years, prosthetic joint infections (PJIs) are still a common complication affecting between 0.3 and 1.8% of patients in the case of THPs (Berbari et al., 1998 [already cited]; Lidgren, 2001 [already cited]) and between 0.5 and 5% of patients in the case of TKPs (Johnson et Bannister, 1986, The outcome of infected arthroplasty of the knee, J Bone Joint Surg 68:289-291; Bengtson et Knutson, 1991, The infected knee arthroplasty, A 6-year follow-up of 357 cases, Acta Othop Scand 62:301-311; Eveillard et al, 2002, Risque infectieux après implantation de prothèses de genou, Etude des infections profondes pour une série continue de 210 prothèses totales de genou en première intention, B E H No. 13). These rates are even higher when it comes to replacement. Infection may occur at any time after implantation of the prosthesis. In a large American study of more than 25,000 patients who have a THP or a TKP, the average period of time between implanting the prostheses and diagnosis of infection was 512 days, with periods ranging from 3 days to nearly 20 years and being distributed as follows: 20% of infections diagnosed within 3 months following implantation, 40% between 3 months and 2 years, and 40% beyond 2 years (Berbari et al., 1998 [already cited]).

PJI is a dangerous complication, resulting in the need for one or more revision surgeries in combination with long-term antibiotherapy, however, long-term functional handicap, a risk of amputation or even death may also occur (Segawa et al, 1999, Infection after total knee arthroplasty, J Bone Joint Surg Am 81:1434-1445). The socio-economic impact of a PJI is also extremely high, with an estimated cost of more than 50,000 dollars per case (Sculco, 1995, The economic impact of infected joint arthroplasty, Orthopedics 18:871-873).

Staphylococci

Bacteria of the Staphylococcus genus are stationary, non-spore-forming, catalase-positive, oxidase-negative, gram-positive cocci grouped together in grape-like clusters. Observed by Pasteur in 1879 in furuncle pus, staphylococci owe their name to Ogsten (1881) who isolated them in acute chronic abscesses.

S. aureus (more commonly known as golden staph) is generally distinguished from other species of staphylococci. Unlike S. aureus these other species do not produce any coagulase enzyme and, for this reason, are grouped separately under the term “coagulase-negative staphylococci” (CNSs).

Habitat of Staphylococci

The natural habitat of S. aureus is humans and warm-blooded animals. In humans, S. aureus preferably resides in nasal mucous; up to 30% of adults permanently harbour S. aureus in their nostrils and 50% harbour it intermittently. Apart from the nose, S. aureus also resides on the skin and, in particular, in moist regions (armpits, perineum) and on the hands. Small amounts of S. aureus can also be found in the intestine. Lastly, the immediate environment of a human is also a source of potential contamination owing to the persistence of S. aureus in the external environment once it has been eliminated.

CNSs are the main commensals of skin together with coryne bacteria and propionibacteria. The density of colonisation is greater in moist regions, such as the anterior portion of the nostrils, the perineum, the armpits and the inguinal folds. Intra-human or inter-human transmission generally occurs by direct contact (for example via the hands). More rarely, transmission may be indirect from an environmental source (clothing, sheets, medical equipment).

Normally present in large quantities on skin and in mucosae, S. epidermidis and the other CNSs may contaminate superficial samples or samples obtained by transcutaneous puncture, such as blood cultures, or even deep perioperative samples taken during surgery. Consequently, CNSs are only considered responsible for an infection if this bacteria is found multiple times in samples taken independently.

Role of Staphylococci in Human Pathology

S. aureus is responsible for many different infections. Cutaneo-mucosal infections, such as folliculitis, impetigo, furuncles, anthrax, panaris, cellulitis, sinusitis or otitis are the most common. These infections may be complicated by the loco-regional extension or hematogenous diffusion of the bacteria. S. aureus thus causes septicaemia, endocarditis, pneumopothy, ostheomyelitis, arthritis and meningitis. These infections may be life-threatening, either per se (for example by attacking a heart valve) or in the case of associated toxic shock.

S. aureus has long been considered the only pathogenic staphylococcus in humans, whilst CNSs were viewed as mere contaminants. The major role of CNSs in human pathology has only recently been established, in particular in patients with joint prostheses, artificial heart valves or implantable devices such as vascular catheters or shunts for diverting cerebrospinal fluid.

S. epidermidis is the CNS which is most frequently isolated in infections on foreign material. Other CNSs which are involved in this type of infection include S. capitis, S. caprae, S. haemolyticus, S. lugdunensis, S. schleiferi, S. simulans and S. warneri.

Staphylococci are the main agents of PJIs and other infections on foreign materials.

Staphylococci are the bacteria most often found in PJIs and other infections on foreign materials, accounting for up to 75% of isolated bacteria, S. aureus and S. epidermidis being the prevalent species (Lew et Waldvogel, 1997 [already cited]). According to studies, the group of CNSs headed by S. epidermidis is alone responsible for 20 to 40% of cases and ranges from being either the most common or second-most common behind S. aureus.

Apart from S. epidermidis, prevalent CNSs are S. capitis, S. caprae, S. haemolyticus, S. lugdunensis, S. schleiferi, S. simulans and S. warneri. Among these species, S. capitis, S. caprae and S. lugdunensis are the main CNSs, apart from S. epidermidis, responsible for prosthetic joint infections and, more generally, osteoarticular infections on foreign material (joint prostheses, osteosynthesis materials) (Rupp et Archer, 1994, Coagulase-negative staphylococci: pathogens associated with medical progress, Clin Infect Dis 19:231-243; Crichton et al, 1995, Subspecies discrimination of staphylococci from revision arthroplasties by ribotyping. J Hosp Infect 30:139-147; Blanc et al, 1999, Infection after total hip replacement by Staphylococcus caprae. Case report and review of the literature, Pathol Biol 47:409-413; Sampathkumar et al, 2000, Prosthetic joint infection due to Staphylococcus lugdunensis. Mayo Clinic Proc 75:511-512; Weightman et al, 2000, Bone and prosthetic joint infection with Staphylococcus lugdunensis, J Infect 40:98-99).

Generally, PJIs and other infections on foreign material caused by S. aureus are most often acute and suppurative owing to the numerous enzymes and toxins produced by this species (Nair et al, 2000, Advances in our understanding of the bone and joint pathology caused by Staphylococcus aureus infection, Rheumatology (Oxford) 39:821-834), whilst CNS infections are mild and are often chronic (Von Eiff et al, 2002, Pathogenesis of infections due to coagulase-negative staphylococci, Lancet Infect Dis 2:677-685). However, this is not always the case: S. aureus infections may often be chronic whilst infections caused by CNSs, such as S. lugdunensis, may develop acutely (Sampathkumar et al, 2000 [already cited]; Weightman et al, 2000 [already cited]).

Characteristics of Staphylococcal Infections on Foreign Material with Biofilm Formation

Staphylococcal infections on foreign material differ from conventional infections by the arrangement of bacteria in the form of biofilm (Costerton et al, 1999, Bacterial biofilms: a common cause of persistent infections, Science 284:1318-22). This process has been described with reference to numerous staphylococci including S. aureus but has been studied, above all, in the case of S. epidermidis (Von Eiff et al, 2002 [already cited]).

Biofilm is a complex three-dimensional structure which is connected to the foreign material and in which the bacteria cells are embedded in a polysaccharide extracellular matrix called slime or glycocalyx (Davey and O′Toole, 2000, Microbial biofilms: from ecology to molecular genetics, Microbiology and Molecular Biology Reviews 64:847-867). This specific structure may be formed by bacteria of the same species or of different species (Costerton et al, 1995, Microbial biofilms, Ann Rev Med 49:711-745; Watnick and Kolter, 2000, Biofilms, city of microbes. J Bacteriol 182:2675-2679). In comparison with their living consgeners in free (or ‘planctonic’) form, these bacteria are in a state of quiescence indicated by a low level of metabolic activity (Yao et al, 2005, Genomewide analysis of gene expression in Staphylococcus epidermidis biofilms: insights into the pathophysiology of S. epidermidis biofilms and the role of phenol-soluble modulins in formation of biofilms, J Infect Dis 191:289-298).

Infections on foreign material associated with biofilm formation have a number of features which distinguish them completely from conventional tissue infections. These infections are most often paucibacillary (having few bacteria) and readily polymicrobial (combination of a plurality of species; for example, S. aureus and S. epidermidis or S. epidermidis and one or more other CNSs (Costerton et al, 1995 [already cited]; Watnick et Kolter, 2000 [already cited]). The bacteria have a very slow metabolism which keeps them in a state close to dormancy and the genes which they express are different to those activated in planctonic forms (Yao et al, 2005 [already cited]). The state of dormancy of the bacteria and the presence of the biofilm significantly reduce the inflammatory reaction and the attraction of immune cells at the infection site. (Vuong et al, 2004, Crucial role for exopolysaccharide modification in bacterial biofilm formation, immune evasion, and virulence, J. Biol. Chem, 279, 52:54881-54886; Fux et al, 2003, Bacterial biofilms: a diagnostic and therapeutic challenge, Expert Rev Anti Infect Ther, 1:667-83). Lastly, for the same reasons, the bacteria are largely protected from the action of antibiotics (Costerton et al, 1995 [already cited]).

Current Methods for Diagnosing Staphylococcal Infections in a Laboratory Bacteriological Diagnosis

Nowadays, bacteriological diagnosis of a staphylococcal infection is almost exclusively direct by isolating the bacteria in relevant samples.

Diagnosis is based on the following main steps:

(1) aseptic sampling (to reduce the risk of contamination by way of a simple commensal staphylococcus on the skin) carried out with no concurrent antibiotherapy (after stopping or before starting antibiotic treatment).

(2) microscopic examination which enables common, gram-positive cocci grouped together in grape-like clusters to be observed. This examination is completely insensitive and gives no indication of the species involved.

(3) culture on ordinary agar in the majority of cases or on a selective culture medium, CHAPMAN-type medium (which contains 7% NaCl, mannitol and a pH indicator) if the sample is potentially contaminated by other bacteria.

(4) identification of the bacteria is based on the isolation of the following features:

-   -   catalase (differentiation from streptococcus),     -   anaerobic glucose fermentation (differentiation from         micrococcus),     -   coagulase (differentiation from CNSs),     -   thermostable Dnase (which indicates the S. aureus species),     -   mini identification gallery (manual or automated)         (identification of CNS species)     -   optionally, molecular identification (for example, sequencing of         the sodA gene) (identification of CNS species).

(5) The diagnosis is completed by measuring sensitivity to antibiotics (antibiogram) given the frequency of resistance of staphylococci, in particular in the case of hospital strains. The profile of sensitivity to antibiotics is also beneficial, although imperfect, for comparing different strains (for true typing it is necessary to use molecular techniques such as pulse field gel electrophoresis or multilocus sequence typing).

The main drawback relates to the interpretation of the culture results since staphylococci are common contaminants. The general rule applied in order to establish a diagnosis of infection is as follows:

S. aureus: at least one positive relevant sample (for example a blood culture),

CNS: at least two independent relevant samples (for example two blood cultures taken at two different times) which are positive for the same bacterium (i.e, in standard practice a bacterium of the same species and having the same sensitivity to antibiotics).

This threshold of two positive samples in the case of CNSs has recently been called into question within the context of PJIs as it is considered to be too nonspecific, and some authors maintain that, from now on, a threshold of three positive perioperative samples will be necessary to diagnose PJI caused by CNS (Atkins et al, 1998, Prospective evaluation of criteria for microbiological diagnosis of prosthetic-joint infection at revision arthroplasty, J Clin Microbiol 36:2932-2939).

Serological Diagnosis

Nowadays, indirect diagnosis of staphylococcal infection by identifying circulating antibodies is largely undeveloped and is only relevant to the diagnosis of some severe S. aureus infections outside foreign material: endocarditis, septicaemia, haematogenous osteoarticular infections (Söderquist et al, 1993, Staphylococcal a-toxin in septicaemic patients; detection in serum, antibody response and production in isolated strains, Serodiagn Immunother Infect Dis 5:139-144; Nordin et al, 1995, Antibody response in patients with osteomyelitis of the mandible, Oral Surg Oral Med Oral Pathol Oral Radiol Endod 79:429-435; Kanclerski et al, 1996, Serum antibody response to Staphylococcus aureus enterotoxins and TSST-1 in patients with septicaemia, J Med Microbiol 44:171-177; Colque-Navarro et al, 1998, Antibody response in Staphylococcus aureus septicemia—a prospective study. J Med Microbiol 47:217-225; Colque-Navarro & Möllby, 1999, Usefulness of staphylococcal serology. J Med Microbiol 48:107-109; Ellis et al, 2003, Role of staphylococcal enterotoxin A in a fatal case of endocarditis, J Med Microbiol 52:109-112).

Current tests are based on the identification of antibodies directed against antigens specific to S. aureus or those produced by S. aureus, for example anti-α-toxin antibodies (or alpha antistaphylolysins), anti-β-ribitol teichoic acid, anti-enterotoxins and anti-staphylococcal toxic shock syndrome toxin 1 (anti-TSST1), and anti-capsular antibodies. The antibodies are detected by haemolysis inhibition, by electrosyneresis or by ELISA (Bornstein et al, 1992, Immune response to staphylococcal toxins and ribitol teichoic acid in Staphylococcus aureus infections, Med Microbiol Lett 1:111-119; Christensson et al, 1993, Diagnosing Staphylococcus aureus endocarditis by detecting antibodies against S. aureus capsular polysaccharides types 5 and 8, J Infect Dis 163:530-533; Kanclerski et al, 1996 [already cited]). These tests are largely insensitive and nonspecific and give variable results depending on the strains involved, in particular depending on the toxins which they produce (for example, greater response for positive enterotoxin B and/or C strains than for positive enterotoxin A and/or TSST1 strains) (Kanclerski et al, 1996 [already cited]). Lastly, there are no tests for identifying the class of the antibodies produced, and in particular whether they are IgG or IgA antibodies.

Both S. aureus and S. epidermidis or other CNSs are commensal bacteria commonly found in humans (nasal membrane for S. aureus and skin for S. epidermidis and other CNSs) and identifying the antigens indicating infection is difficult. This difficulty has been confirmed by laboratory tests carried out by the applicant in which numerous staphylococcal antigens were not established as infection markers, the controls responding in the same proportions as the infected samples.

Diagnosis and Monitoring of Staphylococcal PJIs

It is vital to be able to diagnose a PJI with certainty. In fact, treatment of a PJI, which is involved and costly, is associated with a significant impact on joint function and involves serious risks. Generally, treatment consists of extensive and complicated surgical debridement together with long-term tailored antibiotherapy. The main surgical options are replacing the prosthesis in a one-stage process or debridement and retention of the prosthesis and re-implantation of the prosthesis in two stages, which requires longer periods of hospitalisation (Garvin and Hanssen, 1995, Current concepts review. Infection after total hip arthroplasty. Past, present, and future, J Bone Joint Surg 77-A:1576-1588). The mortality rate associated with surgical procedure for PJI ranges from 0.4 to 1.2% for patients aged 65 and from 2 to 7% for patients aged 80 (Lentino, Prosthetic joint infections: bane of orthopedists, challenge for infectious disease specialists, Clin Infect Dis 36:1157-1161).

The risk of failure by way of infection is greater after revision surgery on PJIs, rising on average from 10 to 40% depending on location, the severity of lesions and the type of surgical treatment. Failure is not always due to infection and, on the other hand, may involve another bacteria other than that which caused the first episode of PJI (associated bacteria not found in perioperative samples or bacteria inoculated accidentally during revision surgery).

A follow-up serological test makes it possible to give an early diagnosis of failure by identifying the nature of the infection and the bacteria involved.

In cases not involving acute or hyperacute PJIs, there are currently no tests which make it possible to make a reliable pre-operative diagnosis of PJI and, in particular, to differentiate a PJI from aseptic loosening, which is treated by simply exchanging the prosthesis in a one-stage process and which does not require any antibiotherapy. The clinical signs are misleading: pain and inflammation are not specific to infection and fever is usually absent. Simple radiography is insensitive and the abnormalities indicating the presence of an infection take too long to appear. Biological markers of inflammation, such as erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP), are insensitive and nonspecific.

Nowadays, diagnosis of PJI can thus only be made with certainty by culturing perioperative samples or fluid aspirate, which involves a surgical procedure carried out under general anaesthetic (in some cases it is also possible to obtain true-cut-type samples without surgery but under general anaesthetic).

This method poses several drawbacks:

it is not currently possible to give a pre-operative diagnosis of PJI or even to establish which bacterium or bacteria are involved,

the methods for culturing perioperative samples are not standardised and recent studies have shown that conventional methods lack sensitivity (Tunney et al, 1999. Detection of prosthetic hip infection at revision arthroplasty by immunofluorescence microscopy and PCR amplification of the bacterial 16S rRNA gene, J Clin Microbiol 37:3281-3290),

the time required for culturing is particularly long in chronic cases,

interpretation of the culture results remains controversial: the threshold of at least three independent positive samples suggested by the OSIRIS group, Oxford provides excellent specificity (Atkins et al, 1998 [already cited]), but may lack sensitivity, in particular when samples are prepared in sub-optimal conditions.

None of the current diagnostic methods uses purified antigens to indicate a staphylococcal infection on a joint prosthesis and current serological methods do not allow follow-up treatment or post-implantation diagnosis to be carried out.

In this field there is thus an extreme need for a serological diagnosis method in order to be able to carry out quick, cheap and non-invasive tests. Ideally, these tests will make it possible to identify the bacterium or bacteria involved and, in particular, will make it possible to distinguish S. aureus, which has a significant ability to destroy tissue, from other staphylococci.

Use of these tests may also make it possible to make an early diagnosis of PJI and thus enable better surgical management at an early stage of infection. This may be achieved by long-term serological monitoring, that is to say monitoring over a substantial period of time, of patients after prosthetic implantation (post-implantation diagnosis), in particular in patients having a higher risk of PJI.

Lastly, in the future, if vaccinal approaches have been developed to prevent staphylococcal PJIs, in particular but not exclusively, those caused by S. aureus, tests of this type will be vital for detecting vaccination failures.

The object of the present invention is to overcome the drawbacks presented by the absence of serological tests enabling a staphylococcal infection on foreign material, in particular on a joint prosthesis, to be isolated by detecting circulating antibodies.

Another object of the present invention is to enable the detection of circulating antibodies which are directed against bacteria which are found in a state of dormancy and are protected from the immune system by being present within a biofilm. A further object of the invention is to enable diagnosis of polymicrobial staphylococcal infections (that is to say those involving a plurality of different species).

An additional object of the invention is to enable a more accurate and more comprehensive analysis owing to the detection of different antibody isotopes specific to polypeptides.

DEFINITIONS

The following definitions are given so as to facilitate the understanding of specific terms used within the description.

“Polynucleotide” means a polyribonucleotide or a polydeoxyribonucleotide which may be modified or unmodified DNA or RNA.

The term polynucleotide includes, in an non-limiting manner, single strand or double strand DNA, DNA formed of a mixture of one or more single strand regions and of one or more double strand regions, DNA which is a mixture of single strand regions, double strand regions and/or triple strand regions, single strand or double strand RNA, RNA formed of a mixture of one or more single strand regions and of one or more double strand regions, and hybrid molecules comprising DNA and RNA which may include single strand regions, double strand regions and/or triple strand regions or a mixture of single strand and double strand regions. The term polynucleotide may also include RNA and/or DNA comprising one or more triple strand regions. Strands in these regions may originate from the same molecule or from different molecules. Consequently, DNA or RNA with a backbone modified for reasons of stability or otherwise are included in the term polynucleotides. Polynucleotide also means DNA and RNA containing one or more modified bases. Modified base means, for example, unusual bases such as inosine. The term polynucleotide also includes chemically, enzymatically or metabolically modified polynucleotides. Polynucleotides also include short polynucleotides, such as oligonucleotides.

“Polypeptide” means a peptide, an oligopeptide, an oligomer or a protein comprising at least two amino acids joined together by a normal or modified peptide bond.

The term polypeptide includes short chains, known as peptides, oligopeptides and oligomers, and long chains known as proteins.

A polypeptide may be formed of amino acids other than the 20 amino acids coded by human genes. A polypeptide may also be formed of amino acids modified by natural processes, such as by the post-translational maturation process or by chemical processes which are well known to the person skilled in the art. The same type of modification may be present at a plurality of locations on the polypeptide and anywhere within the polypeptide: in the peptide backbone, in the amino acid chain or even at the carboxy-terminal or amino-terminal ends.

A polypeptide may be branched following ubiquitination or cyclic with or without branching. These types of modification may be the result of a natural or synthetic post-translational process, these processes being well known to the person skilled in the art.

Modification of a polypeptide means, for example, acetylation, acylation, ADP-ribosylation, amidation, covalent binding of flavin, covalent binding of a heme, covalent binding of a nucleotide or of a nucleotide derivative, covalent binding of a lipid or of a lipid derivative, covalent binding of a phosphatidylinositol, covalent or non-covalent cross linking, cyclisation, formation of a disulphide bond, demethylation, the formation of cysteine, the formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, the formation of a GPI anchor, hydroxylation, iodisation, methylation, myristoylation, oxidation, the proteolytic process, phosphorylation, prenylation, racemisation, seneloylation, sulphation, amino acid addition such as arginylation or ubiquitination (PROTEINS STRUCTURE AND MOLECULAR PROPERTIES, 2^(nd) Ed., T. E. Creighton, W.H. Freeman and Company, New York (1993) and Wold, F., Posttranslational Protein Modifications: Perspectives and Prospects, pgs 1-12 in POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS, B. C. Johnson, Ed., Academic Press, New York (1983); Seifter et al., Meth. Enzymol. 182:626-646 (1990) and Rattan et al., Protein Synthesis: Posttranslational Modifications and Aging, Ann. N.Y. Acad. Sci. 663:48-62 (1992)).

“Percentage identity” between two polynucleotide or polypeptide sequences means the percentage of identical nucleotides or amino acids in the two sequences to be compared and is obtained after achieving the best alignment possible, this percentage being purely statistical and the differences between the two sequences being randomly distributed over their entire length. Comparisons between two polynucleotide or polypeptide sequences are conventionally carried out by comparing these sequences after having optimally aligned them, said comparison being carried out per segment or per “comparison window” in order to identify and compare the local regions with sequence similarity. This comparison may be carried out by means of a program, for example the EMBOSS-Needle program (Needleman-Wunsch global alignment) using the BLOSUM62 matrix/Gap opening penalty 10.0 and Gap extension penalty 0.5 (Needleman et Wunsch (1970), J. Mol. Biol. 48, 443-453 and Kruskal, J. B. (1983), An overview of sequence comparison, In D. Sankoff and J. B. Kruskal, (ed), Time warps, string edits and macromolecules: the theory and practice of sequence comparison, pp. 1-44 Addison Wesley).

The percentage identity is calculated by determining the number of identical positions for which the nucleotide or the amino acid is identical between the two sequences, by dividing this number of identical positions by the total number of positions within the comparison window and by multiplying the result by 100.

A polynucleotide having, for example, an identity of at least 95% with the polynucleotide of SEQ ID No. 1 is thus a polynucleotide comprising, at most, 5 modified nucleotides out of 100 nucleotides compared with said sequence. In other words, up to 5% of the nucleotides in the sequence of SEQ ID No. 1 can be deleted or substituted by another nucleotide, or up to 5% of the total number of nucleotides in the sequence of SEQ ID No. 1 may be inserted into said sequence. These modifications may be located at the 3′ and/or 5′ ends, or anywhere between these ends, at one or more locations.

Similarly, a polypeptide having an identity of at least 95% with the polypeptide of SEQ ID No. 2 is a polypeptide comprising, at most, 5 modified amino acids out of 100 amino acids compared with said sequence. In other words, up to 5% of the amino acids in the sequence of SEQ ID No. 2 can be deleted or substituted by another amino acid or up to 5% of the total number of amino acids in the sequence of SEQ ID No. 2 may be inserted into said sequence. These changes to the sequence may be located at the amino-terminal and/or carboxy-terminal positions of the amino acid sequence or anywhere between these terminal positions, at one or more locations. (Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987).

With regard to the term “similarity”, this is calculated in the same way as identity except that amino acids which are not identical but which have common physico-chemical characteristics are considered to be identical.

“Host cell” means a cell which has been transformed or transfected, or is capable of being transformed or transfected, by an exogenous polynucleotide sequence.

“Culture medium” means the medium in which the polypeptide of the invention is purified. This medium may be formed by the extracellular medium and/or the cellular lysate. Methods which are well known to the person skilled in the art also make it possible restore the active conformation of the polypeptide if the conformation of said polypeptide was modified during isolation or purification.

“Function” means the biological activity of a polypeptide or of a polynucleotide.

The function of a polypeptide in accordance with the invention is that of a Staphylococcus epidermidis and/or Staphylococcus aureus and/or Staphylococcus caprae antigen, and the function of a polynucleotide in accordance with the invention is that of coding said polypeptide. The function of a combination of antigens is to make it possible to diagnose an infection on foreign material and, in particular, on an osteoarticular prosthesis, but also to carry out post-implantation follow-up checks, therapeutic follow-up checks and, lastly, to recognise whether an active or acute infection is involved, for example by detecting different antibody isotopes.

“Antigen” means any compound which, either alone or in combination with an adjuvant or carrier, is capable of inducing a specific immune response. This definition also includes any compound exhibiting structural similarity with said antigen capable of inducing an immunological response directed against said antigen.

“Structural similarity” means a similarity of both the primary structure (sequence) and of the secondary structure (structural elements), of the tertiary structure (three-dimensional structure) or of the quaternary structure (association of a plurality of polypeptides in a single complex) (BIOCHEMISTRY, 4^(th) Ed, L. Stryer, New York, 1995).

A “variant” of what is known as an initial polynucleotide or of what is known as an initial polypeptide means, respectively, a polynucleotide or a polypeptide which differs therefrom by at least one nucleotide or one amino acid, but which maintains the same intrinsic properties, that is to say the same function.

A difference in the polynucleotide sequence of the variant may or may not alter the amino acid sequence of the polypeptide which it codes compared with an initial polypeptide. However, by definition, these variants must confer the same function as the initial polynucleotide sequence, for example code a polypeptide having an antigenic function.

The variant polynucleotide or variant polypeptide generally differs from the initial polynucleotide or initial polypeptide by one (or more) substitutions, additions, deletions, fusions or truncations or by a combination of a plurality of these modifications. An unnatural variant of an initial polynucleotide or of an initial polypeptide may be obtained, for example, by site-directed mutagenesis or by direct synthesis.

A “polynucleotide sequence complementary to the polynucleotide sequence” is defined as a polynucleotide which may be hybridised with said polynucleotide sequence under stringent conditions.

Generally, but not necessarily, “stringent conditions” means chemical conditions enabling hybridisation when the polynucleotide sequences have an identity of at least 80%.

These conditions may be obtained in accordance with methods which are well known to the person skilled in the art.

“Antibodies” means humanised, single-chain, chimeric monoclonal and polyclonal antibodies as well as Fab fragments, including products of Fab or immunoglobin expression library. It is also possible to use other immunospecific molecules in place of antibodies, for example T-cell receptors (TCRs) as recently described (Li et al, 2005, Directed evolution of human T-cell receptors with picomolar affinities by phage display, Nat Biotechnol, 23:349-54) or molecules selected for their specific binding ability, for example by directed evolution (see for example Conrad and Scheller. 2005. Considerations on antibody-phage display methodology, Comb Chem High Throughput Screen, 8:117-26).

An immunospecific antibody may be obtained by administering a given polypeptide to an animal followed by recovery of the antibodies produced by said animal by way of extraction from its bodily fluids. A variant of said polypeptide, or host cells expressing said polypeptide may also be administered to the animal.

The term “immunospecific” applied to the term antibody, in relation to a given polypeptide, means that the antibody has a greater affinity for this polypeptide than for other polypeptides known from the prior art.

“Positive” serum means a serum containing antibodies produced following an S. epidermidis or S. aureus infection on a joint prosthesis and identified by way of their binding to the polypeptides (antigens) of the invention.

“Sensitivity” means the proportion of infected patients diagnosed in accordance with the prior art and said to be positive by way of the diagnostic procedure according to the invention.

“Specificity” means the proportion of blood donors, tested as controls, who underwent the diagnostic procedure in accordance with the invention and who were said to be negative by way of the diagnostic procedure according to the invention.

The present invention achieves the objects detailed above by providing novel polynucleotides and novel polypeptides as well as fragments which have proven to be more relevant and/or more sensitive and/or more specific than the entire protein.

The invention relates to the in vitro use of at least one of the proteins of the sequence of SEQ ID No. 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34 or 36, of part or variants of said protein, of host cells comprising vectors including a polynucleotide coding at least one of said proteins or a variant of said proteins, in the production of antibodies and within the field of in vitro diagnosis of Staphylococcus epidermidis and/or S. aureus. The invention also relates to a diagnostic kit and a pharmaceutical composition.

Use of Polypeptides

The applicant's laboratory is aware of polypeptides produced by S. epidermidis or S. aureus which do not allow prognosis of an infection on foreign material, in particular on a joint prosthesis (for example S. epidermidis recombinant protein “Thimet oligopeptidase-like protein” (Q8CPS6).

However, the applicant unexpectedly found that a prognosis of this type is in fact possible by using other polypeptides produced by S. epidermidis or S. aureus specifically identified by the applicant, and even by using polypeptide fragments produced by S. epidermidis or S. aureus which, when complete, do not allow this prognosis.

The identification of the polypeptides according to the invention is the result of close examination and in-depth studies and was not possible using the sequences produced by the genome research programmes into S. epidermidis or S. aureus.

The present invention thus relates to the use, in the production of antibodies and within the field of in vitro diagnosis of Staphylococcus epidermidis and/or S. aureus infections, of at least one polypeptide comprising:

amino acid sequence of SEQ ID No. 2 (known as protein E4), coded by polynucleotide sequence of SEQ ID No. 1; or

-   -   amino acid sequence of SEQ ID No. 4 (known as protein 2B6),         coded by polynucleotide sequence of SEQ ID No. 3; or     -   amino acid sequence of SEQ ID No. 6 (known as protein F2), coded         by polynucleotide sequence of SEQ ID No. 5; or     -   amino acid sequence of SEQ ID No. 8 (known as protein 3F7),         coded by polynucleotide sequence of SEQ ID No. 7; or     -   amino acid sequence of SEQ ID No. 10 (known as protein 2D6B1),         coded by polynucleotide sequence of SEQ ID No. 9; or     -   amino acid sequence of SEQ ID No. 12 (known as protein JR7),         coded by polynucleotide sequence of SEQ ID No. 11; or     -   amino acid sequence of SEQ ID No. 14 (known as protein JR12),         coded by polynucleotide sequence of SEQ ID No. 13; or     -   amino acid sequence of SEQ ID No. 16 (known as protein JR5),         coded by polynucleotide sequence of SEQ ID No. 15; or     -   amino acid sequence of SEQ ID No. 18 (known as protein 3A7),         coded by polynucleotide sequence of SEQ ID No. 17; or     -   amino acid sequence of SEQ ID No. 20 (known as protein 3B6),         coded by polynucleotide sequence of SEQ ID No. 19; or     -   amino acid sequence of SEQ ID No. 22 (known as protein 3D5),         coded by polynucleotide sequence of SEQ ID No. 21; or     -   amino acid sequence of SEQ ID No. 24 (known as protein 3E5),         coded by polynucleotide sequence of SEQ ID No. 23; or     -   amino acid sequence of SEQ ID No. 26 (known as protein 3F3),         coded by polynucleotide sequence of SEQ ID No. 25; or     -   amino acid sequence of SEQ ID No. 28 (known as protein 3G3),         coded by polynucleotide sequence of SEQ ID No. 27; or     -   amino acid sequence of SEQ ID No. 30 (known as protein 3H3),         coded by polynucleotide sequence of SEQ ID No. 29; or     -   amino acid sequence of SEQ ID No. 32 (known as protein 3H4),         coded by polynucleotide sequence of SEQ ID No. 31; or     -   amino acid sequence of SEQ ID No. 34 (known as protein 3D7),         coded by polynucleotide sequence of SEQ ID No. 33; or     -   amino acid sequence of SEQ ID No. 36 (known as protein 3C7),         coded by polynucleotide sequence of SEQ ID No. 35.

The present invention also relates to the use of at least one polypeptide comprising:

a) part of the amino acid sequence of SEQ ID No. 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34 or 36 having the same function as said sequence, or

b) an amino acid sequence having at least 60% identity, preferably at least 80% identity and most preferably at least 90% identity with one of the amino acid sequences of SEQ ID No. 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34 or 36 or with part of the sequence defined under a), and having the same function as said sequence.

The polypeptides in accordance with the invention may thus comprise variants of amino acid sequences of SEQ ID No. 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34 or 36.

The polypeptide sequence of SEQ ID No. 4, known as protein 2B6, coded by the sequence of SEQ ID No. 3, comprises amino acids 1 to 184 of the sequence of SEQ ID No. 2 and has the same function as the sequence of SEQ ID No. 2.

The polypeptide sequence of SEQ ID No. 6 (known as protein F2), coded by the polynucleotide sequence of SEQ ID No. 5, has 60% identity and 78% similarity with the sequence of SEQ ID No. 2.

Other variants of the sequences of SEQ ID Nos. 2, 4, and 6 are, for example, part of the AtlC protein (3F7 (SEQ ID No. 8) for example) coded by the bacterium Staphylococcus caprae.

Owing to the polypeptides defined above, the invention enables detection of antibodies which are produced naturally during staphylococcal infections on joint prostheses.

The invention further relates to the use of polypeptides according to the invention to periodically detect, in vitro, antibodies directed against S. epidermidis and/or S. aureus and thus to monitor the progression of the pathology and the effect of treatment given to a patient.

The biological samples tested may be samples of blood, urine, saliva, fluid obtained via serological puncture (for example cerebrospinal fluid, pleural fluid or joint fluid) or of one of their constituents (for example serum).

A Staphylococcus epidermidis and/or S. aureus infection is diagnosed in vitro, for example using conventional tests for testing immunological reactions, such as ELISA or Western Blot tests. These tests use one of the polypeptides according to the invention which bonds, specifically, to any serum antibodies directed against Staphylococcus epidermidis and/or S. aureus present in the biological samples.

Use of Expression Vectors and Host Cells

The present invention also relates to the use of a polypeptide prepared by culturing a host cell comprising a recombinant vector having, inserted, a polynucleotide coding said polypeptide.

Numerous expression systems may be used, such as chromosomes, episomes and derived viruses. More particularly, the recombinant vectors used may be derived from bacterial plasmids, transposons, yeast episomes, insertion elements, chromosomal elements of yeasts, viruses such as baculoviruses, papillonna viruses such as SV40, vaccinia viruses, adenovirusus, fox pox viruses, pseudorabies viruses, and retroviruses.

These recombinant vectors may also be derivatives of cosmids or phagemids. The polynucleotide sequence may be inserted into the recombinant expression vector by methods well known to the person skilled in the art.

The recombinant vector may comprise polynucleotide sequences for monitoring the regulation of the polynucleotide expression as well as polynucleotide sequences enabling expression and transcription of a polynucleotide according to the invention and translation of a polypeptide according to the invention, these sequences being selected as a function of the host cells used.

The introduction of the recombinant vector into a host cell may be carried out in accordance with methods which are well known to the person skilled in the art, such as transfection by calcium phosphate, transfection by cationic lipids, electroporation, transduction or infection.

The host cells may be, for example, bacterial cells, such as streptococcal cells, staphylococcal cells, Escherichia coli or Bacillus subtilis cells; fungus cells, such as yeast cells and Aspergillus cells; Streptomyces cells; insect cells, such as Drosophilia S2 and spodoptera Sf9 cells; animal cells, such as CHO, COS, HeLa, C127, BHK, HEK 293 cells or even vegetable cells.

The polypeptide may be purified from host cells in accordance with methods which are well known to the person skilled in the art, such as precipitation using chaotropic agents, such as salts, in particular ammonium sulphate, ethanol, acetone or tricholoroacetic acid, or by means such as acid extraction, ion exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography or exclusion chromatography.

Use of Polynucleotides

The present invention also relates to the use, in the production of antibodies and in the diagnosis of a Staphylococcus epidermidis and/or aureus infection, of at least one polynucleotide comprising the polynucleotide sequence of SEQ ID No. 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33 or 35, coding, respectively, protein 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34 or 36.

The invention also relates to the use of at least one polynucleotide comprising:

a) part of the sequence of SEQ ID No. 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33 or 35, and having the same function as said sequence, or

b) a polynucleotide sequence having at least 60% identity, preferably at least 80% identity, and most preferably at least 90% identity with the polynucleotide sequence of SEQ ID No. 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33 or 35 or with the sequence part as defined under a), and having the same function as said sequence, or

c) a polynucleotide sequence complementary to the polynucleotide sequence of SEQ ID No. 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33 or 35 or to the sequence part defined under a) or to the sequence defined under b).

The polynucleotide sequence of SEQ ID No. 3 comprises nucleotides 1 to 552 of the sequence of SEQ ID No. 1 and has the same function as said sequence.

The polynucleotide sequence of SEQ ID No. 5 (known as F2 and extracted from the Staphylococcus aureus genome) is a variant of the sequence of SEQ ID No. 1.

Other variants are, for example, polynucleotide sequences coding proteins of the autolysin family (for example the sequence of SEQ ID No. 7, a variant of the sequence of SEQ ID No. 1 coding part of the AtlC protein, known as 3F7 and present in the Staphylococcus caprae bacterium). The polynucleotides according to the invention may thus comprise variants of one of the polynucleotide sequences of SEQ ID No. 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33 or 35.

The polynucleotides of the invention may be obtained by standard DNA or RNA synthesis methods.

The polynucleotides according to the invention may also comprise polynucleotide sequences, such as the non-coding 5′ and/or 3′ sequences, for example transcript sequences, untranslated sequences, splicing signal sequences, polyadenylated sequences, ribosome-binding sequences or even RNAm stabilising sequences.

Use of the Antibodies According to the Invention

The invention also relates to the use of antibodies, according to the invention, for in vitro detection in biological samples of the presence of S. epidermidis and/or S. aureus antigens.

The invention further relates to the use of antibodies according to the invention to periodically detect, in vitro, S. epidermidis and/or S. aureus antigens and thus to monitor the progression of the pathology and the effect of treatment given to a patient.

Immunospecific antibodies may be obtained by administering a polypeptide according to the invention, one of its fragments, an analogue or an epitopic fragment, or a cell expressing said polypeptide to a preferably non-human mammal, in accordance with methods well known to the person skilled in the art.

In order to prepare monoclonal antibodies, conventional methods for producing antibodies from cellular lines, such as the hybridomal method, the trioma method, the human B cell hybridomal method and the EBV hybridomal method may be used.

Antibody Isotopes and Affinity

Immunoglobulins (or antibodies) are formed of two different polypeptide chains: two light chains (L) of [kappa] or [lambda] isotopes, and two heavy chains (H) of [gamma], [alpha], [mu], [delta] or [epsilon] isotopes. These four chains are covalently bonded by disulphide bonds. The two chain types H or L have regions which contribute to the binding of antigens and may vary greatly from one immunoglobulin to another. These regions determine the affinity of the antibodies for their ligand.

Heavy chain isotopes make it possible to define the class of the immunoglobulin. There are thus five antibody isotopes (IgA, IgM, IgD, IgE and IgG). Sub-classes, for example IgG1, IgG2, IgG3 and IgG4 are defined by the differences in the heavy chain sequence. The different classes of immunoglobulins have their own physico-chemical properties and their synthesis depends directly on the phases and activation levels of the immune response.

In humans, the IgGs are the main class of immunoglobulins: their serum concentration in adults varies from 8 to 16 g/l. Their plasma half-life is approximately three weeks.

IgAs are the second most common class of serum immunoglobulins after IgGs in terms of concentration (2 to 4 g/l). In contrast, they are the predominant class of immunoglobulins in secretions (respiratory, salivary, digestive secretions, etc, milk, colostrum, tears). With regard to structure, IgAs are distinct by existing in a plurality of molecular forms:

in serum, IgAs may be present in the form of monomers (predominant form) or in the form of dimers associated with a J chain (junction chain). The J chain is a cysteine-rich peptide of 137 amino acids (molecular weight: 15,000 Da), of plasmocyte origin; sub-class IgA1 is predominant in serum.

in secretions, IgAs, known as secretory IgAs, are in the form of dimers: they are thus associated with a J chain but they also comprise a secretory component. IgAs produced by B lymphocytes are captured by epithelial cells by a receptor (polyIgR) arranged at the basal pole of the cell. It is during the transfer of IgA through the epithelial cell towards the apical pole of the cell that the secretory component (molecular weight: 70,000 Da) or secretory piece is added. The role of the secretory piece is to protect the secretory IgAs from proteolytic enzymes present in the secretions.

Similarly to IgAs, IgMs may exist in two distinct molecular forms:

a monomeric form: this is the form in which IgMs are synthesised and inserted into the membrane of B lymphocytes;

a pentameric form: this is the form in which IgMs are secreted. The five base monomers are connected by disulphide bonds. Furthermore, a J chain connects the ends of two monomers.

IgDs account for less than 1% of serum immunoglobulins. They are usually coexpressed with IgMs at the surface of B lymphocytes where they appear to play the role of antigen receptors.

In a normal subject IgEs are only present in trace form.

Kinetics of Appearance of Antibodies and Affinity

The kinetics of appearance of specific antibodies and of a given isotope is still not understood well. Generally, B cells known as naïve B cells synthesise different IgMs which constitute a large source of molecules able to bind antigens (Steven A. Frank, Immunology and Evolution of Infectious Disease, (2002), Princeton University Press, Princeton, USA). When first exposed to an antigen, said antigen thus binds with a weak affinity to different IgMs of the immune system. However, this interaction stimulates division of the corresponding naïve B cell. The rapidity of division increases with the strength of the affinity of the IgM which enables an initial selection of the best clones. Furthermore, during division genetic rearrangements allow the affinity of the antibodies to increase. The constant region of the immunoglobulins also changes so as to produce IgGs in the circulatory system and IgAs at mucous surfaces (Steven et Frank 2002, Immunology and Evolution of Infectious Disease, Princeton University Press, Princeton, USA).

The person skilled in the art may thus deduce that the presence of one or more antibody classes and the specific affinity of the antibodies have different implications from a medical diagnostic point of view when differentiating, in the case of recurrent or non-recurrent infections, between an active, acute, chronic, latent and recent infection.

Kits

The invention also relates to in vitro diagnostic kits comprising at least one of the polypeptides according to the invention, or at least one of the polynucleotides coding said polypeptides, as well as in vitro diagnostic kits comprising at least one of the antibodies according to the invention.

Vaccines

The present invention also relates to a pharmaceutical composition which can be used as a vaccine and contains, as an active ingredient, at least one polypeptide according to the invention or a polynucleotide or a recombinant vector or a host cell according to the invention.

EXPERIMENTAL PART A) Protocols for Producing Antigens A.1. Cloning of the Sequence Coding Polypeptides of SEQ ID No. 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34 or 36

Genes coding polypeptide sequences, which are antigens, are obtained by PCR amplification from the genomic DNA of Staphylococcus epidermidis (WHO 12 strain, ATCC 12228), Staphylococcus caprae (ATCC 35538) or Staphylococcus aureus (MU50 strain, ATCC 700699 or MW2) bacteria by using, respectively, specific primers of the sequences of SEQ ID No. 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33 or 35. Specific primers means short nucleotide sequences capable of hybridisation in a specific manner, owing to the base-pairing rule, on the DNA strand or on its complementary strand, these primers being selected by the person skilled in the art so as to include the DNA sequence and to amplify it specifically (for example SEQ ID No. 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33 or 35).

The corresponding fragment thus amplified is cloned into a vector in accordance with conventional methods well known to the person skilled in the art. This vector allows the production of cloned proteins under the control of an isopropyl thiogalactoside (IPTG) inducible promoter. The cloned proteins correspond to the polypeptides of SEQ ID No. 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34 or 36.

A.2. Expression of Proteins

An Escherichia coli strain is transformed by the aforementioned expression vectors. The selected bacteria are cultured overnight at 30° C., with stirring, in 30 ml of Luria Bertani medium (LB, J. Miller, “A short Course in Bacterial Genetics”, Cold Spring Harbor Laboratory Press, 1992) containing ampicillin at a final concentration of 100 μg/ml. The next day, the culture is diluted at a ratio of 1:50 in a final volume of 1 liter of LB medium supplemented with ampicillin at a final concentration of 100 μg/ml and incubated at 30° C. with stirring. When the turbidity of the culture reaches an absorbance value at 600 nm (A600) of approximately 0.7, the production of the protein is induced by isopropyl thiogalactoside (IPTG) at a final concentration of 0.1 mM. The bacteria are harvested by centrifugation (10 minutes at 1400×g and at 4° C.) when the turbidity of the culture reaches an A600 of approximately 1.5.

A.3. Purification of Proteins

After centrifugation, the cells are resuspended in a 20 mM Tris-HCl buffer at pH 8.0 containing sucrose at 0.5 mM, then treated with lysozyme (0.2 g/l) in the presence of 12.5 mM of ethylenediaminetetraacetic acid (EDTA), DNase, RNase and PMSF. The suspension is incubated for 30 minutes at 4° C. and then centrifuged for 10 minutes at 4° C. at 15,500×g. The pellet is frozen at −20° C. for at least one night.

A.4. Example Purification of 3C7 (SEQ ID No. 36)

After thawing, the bacteria are placed in a Mes 25 mM buffer at pH 6.0, then sonicated for 20 seconds in ice, four times. After centrifugation at 15,500×g at 4° C. for 30 minutes, the supernatant is filtered on a membrane with a porosity of 0.22 μm. The filtrate is then deposited on a cation-exchange column (for example 12 ml SP-SEPHAROSE®, Amersham Biosciences). After washing the column, the protein is eluted with a linear gradient of 0 to 1 M of NaCl in Mes 25 mM buffer at pH 6.0 in 20 column volumes. The fractions containing the protein are combined and the proteins are precipitated by ammonium sulphate at a final concentration of 0.6 g/l. The solution is left for at least one night at 4° C. and then centrifuged for 30 minutes at 20,800×g. The pellet is then taken up in the smallest volume possible (generally 300 μl of 50 mM Na₂HPO₄/NaH₂PO₄ buffer at pH 8.0 containing 100 mM NaCl and then deposited on a gel filtration column, for example SUPERDEX® HR75—10/30, Amersham). The eluted fractions containing the protein are combined and glycerol is added until a final concentration of 20% is obtained. The purified proteins are then stored at −20° C. until they are used in the tests.

The concentrations of the proteins are determined spectrophotometrically from the absorption coefficients calculated using the Pace method (Pace et al, 1995, How to measure and predict the molar absorption coefficient of a protein, Protein Science 4, 2411-2423). The purity of the proteins is checked by SDS-PAGE electrophoresis analysis and by mass spectrometry.

B) In vitro Diagnostic Test

Sera obtained from patients having had a documented osteoarticular infection (laboratory collection) caused by:

Staphylococcus epidermidis (at least three positive perioperative samples);

Staphylococcus aureus (at least one positive perioperative sample);

bacteria other than staphylococci (at least three positive perioperative samples) were used.

The control sera were sera obtained from blood donors (laboratory collection).

Example B1 Protocol of the Test for Polypeptides of SEQ ID Nos 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32 and 34 (ELISA)

The binding of the antibodies present in the sera was assessed using ELISA tests. The ELISA plates were left overnight at 4° C. in the presence of 0.5 μg of purified antigen (recombinant protein E4) in a phosphate buffered saline (PBS). After four washes with PBS containing 0.05% polyoxyethylene sorbitan (TWEEN®), the plates were saturated for one hour at 37° C. in PBS-TWEEN containing 5% semi-skimmed milk (250 μl per well). Four new washes were carried out and then 100 μl of each positive serum, at the appropriate dilution ratio (i.e. 1:3000 for E4) in PBS-TWEEN buffer containing 5% semi-skimmed milk, were added to each well. The plate was then left at 25° C. for 30 minutes. After four new washes, goat anti-human immunoglobulin G, M, or A (secondary) antibodies or, simultaneoulsy, goat anti-human immunoglobulin G and/or A and/or M (secondary) antibodies labelled with alkaline phosphatase (for example 170-6462, Biorad) were added for 30 minutes at 25° C. after having been diluted in accordance with the supplier's protocol in PBS-TWEEN buffer containing 5% semi-skimmed milk. Four new washes were carried out and then 100 μl of pNPP (p-nitrophenyl phosphate) substrate, for example A-3469, Sigma were added. The absorbance at 405 nm of each of the wells was measured after incubation for 30 minutes at 37° C.

Results and Interpretation

The tests were carried out on recombinant proteins obtained from independent purifications.

Typical results are shown in Table 1 (results according to the invention for polypeptides E4, F2 and 2D6-B1 with secondary antibodies recognising the total immunoglobulins (Ig G, A, and M) present in the patient sera).

TABLE 1 results (ELISA) obtained using anti-IgGAM antibodies as secondary antibodies Polypeptide tested E4 F2 2D6B1 Percentage of “positive” sera from the 47.0% 50.0% 40.0% 15 sera of patients infected with S. epidermidis diagnosed according to the prior art and who underwent the diagnostic procedure according to the present invention Percentage of “positive” sera from the 26.0% 25.0% 25.0% 16 sera of patients infected with S. aureus diagnosed according to the prior art and who underwent the diagnostic procedure according to the present invention Percentage of “negative” sera from the 95.0% 98.0% 96.8% 96 blood donor sera tested as controls

It can be seen from Table 1 that the polypeptides of the invention may be used to isolate staphylococcal infections on joint prostheses.

Example B2 Results Obtained by Detecting of Antibody Isotypes in Sera (ELISA)

The use of some polypeptides, for example 2D6-B1 (Table 2) to detect immunoglobulins of a specific isotype is of particular relevance.

TABLE 2 Examples of results (ELISA) using anti-IgA antibodies as secondary antibodies Polypeptide tested 2D6B1 Percentage of “positive” sera from the 15 sera of patients 47.0% infected with S. epidermidis diagnosed according to the prior art and who underwent the diagnostic procedure according to the present invention Percentage of “positive” sera from the 16 sera of patients 31.0% infected with S. aureus diagnosed according to the prior art and who underwent the diagnostic procedure according to the present invention Percentage of “negative” sera from the 96 blood donor sera 97.0% tested as controls

It follows that the polypeptides may be used to indicate the presence of some antibody isotypes in the case of staphylococcal infections on joint prostheses.

Example B3 Combination of Polypeptides for in vitro Diagnosis of PJI

The combined use of a plurality of antigens and/or the detection of a plurality of antibody isotypes makes it possible to increase the sensitivity of the method (Tables 3 and 4).

Polypeptide 2B6 is very specific to S. epidermidis infections. In contrast with 2B6, polypeptide 2D6-B1 is not specific to a particular species and “positive” results may be observed with sera from patients having a PJI caused by other species of Staphylococcus (for example S. lugdunensis). This polypeptide is therefore “specific” to the staphylococcus genus and not to a specific species. It is thus possible, by using different polypeptides (or by detecting different antibody isotypes), to differentiate between species.

TABLE 3 Results (ELISA) obtained using combinations of different polypeptides according to the invention to detect immunoglobulins IgG, A or M Polypeptide tested 2B6 2D6B1 2B6 or 2D6B1 Percentage of “positive” sera from 67.0% 40.0% 87.0% the 15 sera of patients infected with S. epidermidis diagnosed according to the prior art and who underwent the diagnostic procedure according to the present invention Percentage of “positive” sera from 11.0% 25.0% 37.5% the 16 sera of patients infected with S. aureus diagnosed according to the prior art and who underwent the diagnostic procedure according to the present invention Percentage of “negative” sera from 99.0% 96.8% 96.0% the 96 blood donor sera tested as controls

TABLE 4 Results (ELISA) obtained by using 2D6B1 as a polypeptide and by detecting antibodies using different secondary antibodies Secondary antibodies used IgA IgG IgG or A Percentage of “positive” sera from 47.0% 40.0% 67.0% the 15 sera of patients infected with S. epidermidis diagnosed according to the prior art and who underwent the diagnostic procedure according to the present invention Percentage of “positive” sera from 31.0% 25.0% 37.0% the 16 sera of patients infected with S. aureus diagnosed according to the prior art and who underwent the diagnostic procedure according to the present invention Percentage of “negative” sera from 97.0% 96.0% 96.0% the 96 blood donor sera tested as controls

Example B4 Identification of PJIs Not Diagnosed by Culturing Perioperative Samples

These tests were carried out using sera from patients who underwent surgery for a suspected staphylococcal infection on a joint prosthesis, but who were considered, from a bacteriological point of view, to be uninfected in accordance with results following culture of deep perioperative samples obtained during revision surgery on the prosthesis (only one or two perioperative samples positive for CNS).

Table 5 shows an example of typical results obtained by detecting the total anti-2D6B1 immunoglobulins in 7 patients having had one or two perioperative samples which were positive for S. epidermidis. (laboratory collection). The control sera were sera obtained from blood donors (laboratory collection).

TABLE 5 Type of prosthesis ELISA value Patient 1 TKP 2.026 Patient 2 THP 0.151 Patient 3 TKP 0.302 Patient 4 THP 0.970 Patient 5 TKP 2.237 Patient 6 THP 0.369 Patient 7 THP 0.465

During the same analysis, 3 of the 89 control sera (blood donors) had an ELISA value≧0.900 (threshold indicating a specificity of 96.6%) and none had an ELISA value≧1.600 (threshold indicating a specificity of 100.0%). The observed response was thus significant in patient 4 and highly significant in patients 1 and 5.

It is has thus been proven that it is possible to detect a significant antibody response to the polypeptides according to the invention in the case of osteoarticular infections on prostheses which have not been diagnosed by culturing perioperative samples.

Example B5 Protocol of the Test for Polypeptides of SEQ ID Nos. 12, 14 and 16 (Western Blot)

For the Western Blot tests, sera obtained from patients having had a documented S. aureus or S. epidermidis infection (laboratory collection) were used.

The control sera were sera obtained from blood donors (laboratory collection) and from patients carrying other infections (laboratory collection). Any possible binding of the antibodies present in these sera was assessed using Western Blot tests on total extracts of bacteria producing polypeptides of SEQ ID Nos 12, 14 and 16.

The nitrocellulose membrane onto which the proteins of the extract were transferred was saturated for 30 minutes using a phosphate buffered saline (PBS) solution containing 3% semi-skimmed milk. After three washes with PBS containing 0.05% polyoxyethyelene sorbitan (TWEEN®), the membrane was exposed to the test serum at the appropriate dilution ratio (i.e. 1:300) in PBS buffer containing 3% semi-skimmed milk, for 45 minutes. After three new washes, goat anti-human immunoglobulin G, M or A (secondary) antibodies or, simultaneously, goat anti-human immunoglobulin G and/or A and/or M (secondary) antibodies labelled with alkaline phosphatase (for example 170-6462, Biorad) were added for 30 minutes after having been diluted according to the supplier's protocol in PBS buffer containing 3% semi-skimmed milk. Three new washes were carried out and then 5-bromo-4-chloro-3-indolyl phosphate and nitroblue tetrazolium were added according to the supplier's instructions until the result was obtained. A “positive” result corresponds to precipitation of the substrate on the membrane at the position of the polypeptides of SEQ ID Nos 12, 14 or 16.

The results of these tests prove the existence of a significant antibody response in the case of osteoarticular infections on foreign material to polypeptides of SEQ ID Nos 12, 14 or 16 and the relevance of these polypeptides and of their associations/combinations for serological diagnosis of this type of infection. In fact, the combination of polypeptides of SEQ ID Nos 12, 14 or 16 is also relevant.

Similar results were obtained for all the polypeptides according to the invention (polypeptides of SEQ ID Nos 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32 and 34).

It has thus been proven, on the one hand, that there is a significant antibody response (IgG and/or IgA) in the case of osteoarticular infections on foreign material and, on the other hand, that the polypeptides according to the invention and their associations/combinations are relevant for the serological diagnosis of this type of infection. In fact, the combination of at least two polypeptides of SEQ ID Nos 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32 and 34 is also relevant. Furthermore, the combination of the results obtained by detection of different antibody isotypes in sera, for each of the polypeptides, is also relevant.

C) Use of the Polypeptides According to the Invention for Therapeutic Follow-Up Checks (Table 6)

For patients in convalescence, the observance of a decrease over time in the ELISA values, obtained by detecting the immunoglobulins (antibodies) present in the sera by way of their binding to antigens 2B6 or 2D6-B1 according to the invention, demonstrates that they are recovering well.

TABLE 6 Progression as a function of the secondary antibody used ELISA value 2D6B1 2B6 Patient 1 anti-IgGAM 0.99 2.3 (+) anti-IgG 0.4 0.51 (+) anti-IgA 0.66 0.34 Patient 1 + 1 year anti-IgGAM 0.44 0.74 anti-IgG 0.27 0.24 anti-IgA 0.31 0.31 Patient 2 anti-IgGAM 1.03 1.43 (+) anti-IgG 0.5 0.46 (+) anti-IgA 1.6 (+) 0.2 Patient 2 + 3 months anti-IgGAM 0.44 0.74 anti-IgG 0.27 0.24 anti-IgA 0.31 0.31 Patient 3 anti-IgGAM 2.27 (+) 1.6 (+) anti-IgG 0.94 (+) 0.5 (+) anti-IgA 0.14 0.19 Patient 3 + 6 months anti-IgGAM 2.41 (+) 0.86 anti-IgG 0.87 (+) 0.22 anti-IgA 0.15 0.19 The ELISA values marked (+) are considered to be positive

In Table 6, the individuals who were initially positive according to the invention have become negative.

Use of the polypeptides according to the invention thus makes it possible to carry out therapeutic follow-up checks, i.e. (i) to assess the effect of treatment and (ii) to monitor the post-operative (or post-implantation) progression of a patient.

D) Optimisation of Antigens and in vitro Diagnostic Tests

The study of fragments in order to improve, antigen performance on the one hand, and polypeptide production on the other is particularly useful for industrial use thereof and for the relevance of the tests.

Example D1 Increase in Sensitivity and Specificity

Table 7 shows the performances of 2B6, which is a fragment of E4, relative to the polypeptide E4.

TABLE 7 Optimisation of the sensitivity and specificity of E4, 2B6; ELISA results using an IgGAM secondary antibody Polypeptide tested E4 2B6 Percentage of “positive” sera from the 15 sera of 47.0% 67.0% patients infected with S. epidermidis diagnosed according to the prior art and who underwent the diagnostic procedure according to the invention Percentage of “negative” sera from the 96 blood 95.0% 99.0% donor sera tested as controls

There is a substantial difference depending on the polypeptide fragments used. This difference was not foreseeable based on the sequences. The sensitivity and specificity of 2B6 (fragment of E4) are thus greater than the entire protein or E4 (Table 7).

The use of antigen 2B6 to detect (total) immunoglobulins A, G and M makes it possible to identify 67% of PJIs caused by S. epidermidis (10 out of the 15 test sera) with 99% specificity (1 in 96 test blood donor sera).

Example D2 Increase in Stability and Production Levels

Furthermore, protein 2B6 does not deteriorate during its production in the host cell or during its purification.

E) Mulitparametric Combination and Evaluation by Syndrome

The combined use of a plurality of polypeptides according to the invention also makes it possible:

-   -   (i) to increase the sensitivity of detection;     -   (ii) to assess the likelihood of the presence of a plurality of         bacteria (for example by using an antigen which is specific to a         bacteria or to a family of bacteria);     -   (iii) to identify the genotype of the strain;     -   (iv) to determine progression of the pathology (by using         specific antigens and antibody isotypes);     -   (v) to carry out therapeutic follow-up checks at reduced cost;         and     -   (vi) to carry out diagnosis per syndrome

In conclusion, the present invention discloses polypeptides having optimum sensitivity and specificity, enabling them to be used as a probe (antigen probe) in tests. The present invention makes it possible, without the need for surgery, to diagnose staphylococcal infections on foreign material, such as osteoarticular prostheses, in particular infections which have not been diagnosed by culturing deep perioperatve samples. 

The invention claimed is:
 1. An in vitro diagnostic method for determining if an individual is infected by bacteria of the Staphylococcus genus, comprising: contacting a biological sample of the individual with a purified protein consisting of SEQ ID NO: 10, measuring the amount of antibodies present in the biological sample that are bound to said protein, and determining whether or not the individual is infected by said Staphylococcus bacteria based upon the measured amount.
 2. The method of claim 1, wherein the biological sample is selected from the group consisting of: blood, serum, urine, saliva, cerebrospinal fluid, pleural fluid, and articular fluid.
 3. An in vitro diagnostic method for determining the presence of antibodies directed against bacteria of the Staphylococcus genus in a biological sample, comprising: contacting the biological sample with a purified protein consisting of SEQ ID NO: 10; and detecting antibodies present in the biological sample that are bound to said protein.
 4. The method of claim 3, wherein the biological sample is selected from the group consisting of: blood, serum, urine, saliva, cerebrospinal fluid, pleural fluid, and articular fluid.
 5. The method of claim 1, wherein the amount of antibodies present in the biological sample that are bound to said protein is measured by immunoassay.
 6. The method of claim 1, wherein the immunoassay is ELISA.
 7. The method of claim 1, wherein the immunoassay is Western blot.
 8. The method of claim 5, wherein, said protein consisting of SEQ ID NO: 10 is present on a surface of a well of an ELISA plate, contacting the biological sample with said protein comprises adding a serum sample from the individual to said well and incubating the ELISA plate for a period of time, and said immunoassay comprises: adding a secondary antibody comprising goat anti-human immunoglobulin labelled with alkaline phosphatase to said well, adding a substrate comprising p-nitrophenyl phosphate to said well, and measuring absorbance of said well at 405 nm.
 9. The method of claim 1, wherein the individual has a joint prostheses.
 10. The method of claim 1, wherein the bacteria of the Staphylococcus genus is at least one of Staphylococcus aureus and Staphylococcus epidermidis.
 11. The method of claim 1, wherein determining whether or not the individual is infected by the Staphylococcus bacteria comprises comparing the amount of bound antibodies from the biological sample to an amount of bound antibodies from one or more control sample.
 12. The method of claim 11, wherein the one or more control sample is a positive control or a negative control.
 13. The method of claim 1, wherein the biological sample is serum.
 14. An in vitro method for detecting a prosthetic joint infection (PJI) caused by bacteria of the Staphylococcus genus in an individual, comprising: contacting a biological sample of the individual with a purified protein consisting of SEQ ID NO: 10, measuring the amount of antibodies present in the biological sample that are bound to said protein, and determining whether or not the individual has the PJI based upon the measured amount.
 15. The method of claim 14, wherein the amount of antibodies present in the biological sample that are bound to said protein is measured by immunoassay.
 16. The method of claim 14, wherein the bacteria of the Staphylococcus genus is at least one of Staphylococcus aureus and Staphylococcus epidermidis.
 17. The method of claim 14, wherein determining whether or not the individual is infected by the Staphylococcus bacteria comprises comparing the amount of bound antibodies from the biological sample to an amount of bound antibodies from one or more control sample. 